# set up =======================================================================
library(here)
library(readr)
library(dplyr)
library(ggplot2)
library(sf)
options(readr.show_col_types = FALSE)
options(dplyr.warnings = FALSE)
# read in the functions files
source(here::here("./R/00_global_funs.R"))
source(here::here("./R/01_plots_functions.R"))
fish_data <- readr::read_csv(
here::here("./data/bati_fish_data_2023-10-04.csv")
) %>%
standardize_names()
seaway_data <- readr::read_csv(
here::here("./data/bati_seaway_distances_to_farms.csv")
)
## New names:
## • `` -> `...1`
site_data <- readr::read_csv(here::here("./data/bati_site_data_2023-10-04.csv"))
farm_activity <- readxl::read_xlsx(here::here("./data/farm_activity.xlsx"))
geo_data <- sf::read_sf(here::here("./data/geo-spatial/shapefile/"))
farm_locs <- readr::read_csv(
here::here("./data/geo-spatial/farm-locations.csv")
)
sampling_locs <- readr::read_csv(
here::here("./data/geo-spatial/bati_site_master_list.csv")
)
head_dists <- readr::read_csv(
here::here("./data/headwater-distances.csv")
)
inventory <- readr::read_csv(
here::here("./data/old-farm-data.csv")
) %>% dplyr::mutate(
date = lubridate::ym(
paste(year, month, sep = "-")
)
)
# some data cleaning ===========================================================
fish_data <- lice_data_clean(fish_data, sampling_locs)
inventory <- inventory[which(inventory$month %in% c(3:6)), ]
# put some initial plots =======================================================
plot_study_area(
geo_data, farm_locs, sampling_locs,
to_save = TRUE
)
## Warning: attribute variables are assumed to be spatially constant throughout
## all geometries
## Saving 7 x 7 in image
## Saving 7 x 7 in image

time_series_lice(
fish_data, sampling_locs, inventory
)
## `summarise()` has grouped output by 'year', 'month'. You can override using the `.groups` argument.
## Saving 7 x 7 in image
## Warning: Removed 5 rows containing missing values (`geom_point()`).
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## Saving 7 x 7 in image
## `summarise()` has grouped output by 'year', 'month'. You can override using the `.groups` argument.
## Saving 7 x 7 in image
## Warning: Removed 5 rows containing missing values (`geom_point()`).
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## Saving 7 x 7 in image
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## Saving 7 x 7 in image
## Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).
## Warning: Removed 2 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## `summarise()` has grouped output by 'year', 'month'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## `summarise()` has grouped output by 'year'. You can override using the `.groups` argument.
## Saving 7 x 7 in image
## Warning: Removed 1 rows containing non-finite values (`stat_smooth()`).
## Warning: Removed 1 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 1 rows containing non-finite values (`stat_smooth()`).
## Removed 1 rows containing missing values (`geom_point()`).
## [[1]]
## Warning: Removed 5 rows containing missing values (`geom_point()`).

##
## [[2]]

##
## [[3]]
## Warning: Removed 5 rows containing missing values (`geom_point()`).

##
## [[4]]

##
## [[5]]
## Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).
## Warning: Removed 2 rows containing missing values (`geom_point()`).

##
## [[6]]

##
## [[7]]
## Warning: Removed 1 rows containing non-finite values (`stat_smooth()`).
## Warning: Removed 1 rows containing missing values (`geom_point()`).

##
## [[8]]
## Warning: Removed 1 rows containing non-finite values (`stat_smooth()`).
## Removed 1 rows containing missing values (`geom_point()`).

maps_with_data(
inventory, fish_data, sampling_locs, farm_locs, geo_data
)
## `summarise()` has grouped output by 'year'. You can override using the
## `.groups` argument.
## Warning: attribute variables are assumed to be spatially constant throughout
## all geometries
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## `summarise()` has grouped output by 'site_code'. You can override using the `.groups` argument.
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Warning: Removed 10 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 9 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 9 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Warning: Removed 9 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 13 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Warning: Removed 13 rows containing missing values (`geom_sf()`)
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Saving 7 x 7 in image
## Warning: Removed 13 rows containing missing values (`geom_sf()`)
## $length

##
## [[2]]

##
## [[3]]

##
## [[4]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[5]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[6]]

##
## [[7]]

##
## [[8]]

##
## [[9]]

##
## [[10]]

##
## [[11]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[12]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[13]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[14]]

##
## [[15]]

##
## [[16]]

##
## [[17]]

##
## [[18]]

##
## [[19]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[20]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[21]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[22]]

##
## [[23]]

##
## [[24]]

##
## [[25]]

##
## [[26]]

##
## [[27]]
## Warning: Removed 10 rows containing missing values (`geom_sf()`)

##
## [[28]]
## Warning: Removed 9 rows containing missing values (`geom_sf()`)

##
## [[29]]
## Warning: Removed 9 rows containing missing values (`geom_sf()`)

##
## [[30]]

##
## [[31]]

##
## [[32]]

##
## [[33]]

##
## [[34]]

##
## [[35]]
## Warning: Removed 9 rows containing missing values (`geom_sf()`)

##
## [[36]]
## Warning: Removed 13 rows containing missing values (`geom_sf()`)

##
## [[37]]
## Warning: Removed 13 rows containing missing values (`geom_sf()`)

##
## [[38]]

##
## [[39]]

##
## [[40]]

##
## [[41]]

##
## [[42]]

##
## [[43]]
## Warning: Removed 13 rows containing missing values (`geom_sf()`)

headwater_distances(
head_dists, fish_data
)
## Saving 7 x 7 in image
## Warning: Removed 6 rows containing missing values (`position_stack()`).
## Warning: Removed 36 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 6 rows containing missing values (`position_stack()`).
## Removed 36 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 6 rows containing missing values (`position_stack()`).
## Removed 36 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 6 rows containing missing values (`position_stack()`).
## Warning: Removed 39 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 7 rows containing missing values (`position_stack()`).
## Warning: Removed 30 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 7 rows containing missing values (`position_stack()`).
## Removed 30 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 7 rows containing missing values (`position_stack()`).
## Removed 30 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 7 rows containing missing values (`position_stack()`).
## Warning: Removed 33 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 11 rows containing missing values (`position_stack()`).
## Warning: Removed 42 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 11 rows containing missing values (`position_stack()`).
## Removed 42 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 11 rows containing missing values (`position_stack()`).
## Removed 42 rows containing missing values (`geom_point()`).
## Saving 7 x 7 in image
## Warning: Removed 11 rows containing missing values (`position_stack()`).
## Warning: Removed 44 rows containing missing values (`geom_point()`).
## [[1]]
## Warning: Removed 6 rows containing missing values (`position_stack()`).
## Warning: Removed 36 rows containing missing values (`geom_point()`).

##
## [[2]]
## Warning: Removed 6 rows containing missing values (`position_stack()`).
## Removed 36 rows containing missing values (`geom_point()`).

##
## [[3]]
## Warning: Removed 6 rows containing missing values (`position_stack()`).
## Warning: Removed 39 rows containing missing values (`geom_point()`).

##
## [[4]]
## Warning: Removed 6 rows containing missing values (`position_stack()`).
## Warning: Removed 36 rows containing missing values (`geom_point()`).

##
## [[5]]
## Warning: Removed 7 rows containing missing values (`position_stack()`).
## Warning: Removed 30 rows containing missing values (`geom_point()`).

##
## [[6]]
## Warning: Removed 7 rows containing missing values (`position_stack()`).
## Removed 30 rows containing missing values (`geom_point()`).

##
## [[7]]
## Warning: Removed 7 rows containing missing values (`position_stack()`).
## Warning: Removed 33 rows containing missing values (`geom_point()`).

##
## [[8]]
## Warning: Removed 7 rows containing missing values (`position_stack()`).
## Warning: Removed 30 rows containing missing values (`geom_point()`).

##
## [[9]]
## Warning: Removed 11 rows containing missing values (`position_stack()`).
## Warning: Removed 42 rows containing missing values (`geom_point()`).

##
## [[10]]
## Warning: Removed 11 rows containing missing values (`position_stack()`).
## Removed 42 rows containing missing values (`geom_point()`).

##
## [[11]]
## Warning: Removed 11 rows containing missing values (`position_stack()`).
## Warning: Removed 44 rows containing missing values (`geom_point()`).

##
## [[12]]
## Warning: Removed 11 rows containing missing values (`position_stack()`).
## Warning: Removed 42 rows containing missing values (`geom_point()`).
